The generation of flexible sparse metrology sample plans includes receiving a full set of metrology signals from one or more wafers from a metrology tool, determining a set of wafer properties based on the full set of metrology signals and calculating a wafer property metric associated with the set of wafer properties, calculating one or more independent characterization metrics based on the full set of metrology signals, and generating a flexible sparse sample plan based on the set of wafer properties, the wafer property metric, and the one or more independent characterization metrics. The one or more independent characterization metrics of the one or more properties calculated with metrology signals from the flexible sparse sampling plan is within a selected threshold from one or more independent characterization metrics of the one or more properties calculated with the full set of metrology signals.